Extensive recoding of dengue virus type 2 specifically reduces replication in primate cells without gain-of-function in Aedes aegypti mosquitoes.

Charles B Stauft,Laura Kramer,Yutong Song,Matthew Brecher,Eckard Wimmer,Emmanuel Asare,Bruce Futcher,Sam H Shen,Steffen Mueller,Oleksandr Gorbatsevych,Anne Payne,Nikos Vasilakis

doi:10.1371/journal.pone.0198303

Abstract

Dengue virus (DENV), an arthropod-borne (“arbovirus”) virus, causes a range of human maladies ranging from self-limiting dengue fever to the life-threatening dengue shock syndrome and proliferates well in two different taxa of the Animal Kingdom, mosquitoes and primates. Mosquitoes and primates show taxonomic group-specific intolerance to certain codon pairs when expressing their genes by translation. This is called “codon pair bias”. By necessity, dengue viruses evolved to delicately balance this fundamental difference in their open reading frames (ORFs). We have undone the evolutionarily conserved genomic balance in the DENV2 ORF sequence and specifically shifted the encoding preference away from primates. However, this recoding of DENV2 raised concerns of ‘gain-of-function,’ namely whether recoding could inadvertently increase fitness for replication in the arthropod vector. Using mosquito cell lines and two strains of Aedes aegypti we did not observe any increase in fitness in DENV2 variants codon pair deoptimized for humans. This ability to disrupt and control DENV2’s host preference has great promise towards developing the next generation of synthetic vaccines not only for DENV but for other emerging arboviral pathogens such as chikungunya virus and Zika virus.

Highlights

Synthetic biology has the potential to revolutionize the rapid development of vaccines to prevent infectious diseases as the research paradigm shifts from empirical to rational design [1,2]
The codon pair scores of the hmin constructs for all three proteins are significantly more negative than that of the wt sequences whereas the scores for insect open reading frames (ORFs) remained almost wild type[17]
We have recoded individually three coding regions of the DENV2 polyprotein according to a master plan: increasing the number of “bad” codon pairs to reduce expression in primate cells while retaining a wild type average of codon pairs for wildtype expression in mosquito cells (Fig 1A)

Summary

Introduction

Synthetic biology has the potential to revolutionize the rapid development of vaccines to prevent infectious diseases as the research paradigm shifts from empirical to rational design [1,2]. Recoding of dengue virus type 2 reduces replication in primate cells without gain-of-function in mosquitoes

Methods

Results

Conclusion